11 results on '"Ghader Bashiri"'
Search Results
2. Convergent pathways to biosynthesis of the versatile cofactor F420
- Author
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Ghader Bashiri and Edward N. Baker
- Subjects
0303 health sciences ,animal structures ,biology ,biology.organism_classification ,Cofactor ,Biosynthetic enzyme ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Biochemistry ,Biosynthesis ,chemistry ,Structural Biology ,biology.protein ,Molecular Biology ,030217 neurology & neurosurgery ,030304 developmental biology ,Archaea - Abstract
Cofactor F420 is historically known as the methanogenic redox cofactor, having a key role in the central metabolism of methanogens, and archaea in general. Over the past decade, however, it has become evident this cofactor is more widely distributed across archaeal and bacterial taxa, suggesting a broader role for F420 in various metabolic and ecological capacities. In this article, we focus on the recent findings that have led to a deeper understanding of F420 biosynthetic enzymes and metabolites across microorganisms.
- Published
- 2020
3. Clusterin is involved in mediating the metabolic function of adipose SIRT1
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Pengcheng Zhang, Daniels Konja, Yiwei Zhang, Aimin Xu, In-Kyu Lee, Jae-Han Jeon, Ghader Bashiri, Alok Mitra, and Yu Wang
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enzymes and coenzymes (carbohydrates) ,Biological sciences ,Cell biology ,Multidisciplinary ,Science ,food and beverages ,lipids (amino acids, peptides, and proteins) ,hormones, hormone substitutes, and hormone antagonists ,Article ,Molecular physiology - Abstract
Summary SIRT1 is a metabolic sensor regulating energy homeostasis. The present study revealed that mice with selective overexpression of human SIRT1 in adipose tissue (Adipo-SIRT1) were protected from high-fat diet (HFD)-induced metabolic abnormalities. Adipose SIRT1 was enriched at mitochondria-ER contacts (MERCs) to trigger mitohormesis and unfolded protein response (UPRmt), in turn preventing ER stress. As a downstream target of UPRmt, clusterin was significantly upregulated and acted together with SIRT1 to regulate the protein and lipid compositions at MERCs of adipose tissue. In mice lacking clusterin, HFD-induced metabolic abnormalities were significantly enhanced and could not be prevented by overexpression of SIRT1 in adipose tissue. Treatment with ER stress inhibitors restored adipose SIRT1-mediated beneficial effects on systemic energy metabolism. In summary, adipose SIRT1 facilitated the dynamic interactions and communications between mitochondria and ER, via MERCs, in turn triggering a mild mitochondrial stress to instigate the defense responses against dietary obesity-induced metabolic dysfunctions., Graphical abstract, Highlights • Adipose SIRT1 triggers mitohormesis and UPRmt, in turn upregulating clusterin • Adipose SIRT1 and clusterin regulate the protein and lipid compositions at MERCs • Adipose SIRT1 and clusterin reinforce UPRmt-mediated anti-ER stress signaling • Adipose SIRT1 dysfunction causes obesity and associated metabolic abnormalities, Biological sciences; Molecular physiology; Cell biology
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- 2022
4. Mechanistic insights into F 420 -dependent glucose-6-phosphate dehydrogenase using isotope effects and substrate inhibition studies
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Mercy Oyugi, Ghader Bashiri, Kayunta Johnson-Winters, and Edward N. Baker
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0301 basic medicine ,Reaction mechanism ,Stereochemistry ,Biophysics ,Glucose-6-Phosphate ,Dehydrogenase ,Glucosephosphate Dehydrogenase ,Biochemistry ,Article ,Citric Acid ,Cofactor ,Analytical Chemistry ,03 medical and health sciences ,Bacterial Proteins ,Kinetic isotope effect ,Organic chemistry ,Enzyme kinetics ,Molecular Biology ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Deuterium Exchange Measurement ,Substrate (chemistry) ,Mycobacterium tuberculosis ,Deuterium ,030104 developmental biology ,biology.protein ,Steady state (chemistry) ,Uncompetitive inhibitor - Abstract
F420-dependent glucose-6-phosphate dehydrogenase (FGD) is involved in the committed step of the pentose phosphate pathway within mycobacteria, where it catalyzes the reaction between glucose-6-phosphate (G6P) and the F420 cofactor to yield 6-phosphogluconolactone and the reduced cofactor, F420H2. Here, we aim to probe the FGD reaction mechanism using dead-end inhibition experiments, as well as solvent and substrate deuterium isotope effects studies. The dead-end inhibition studies performed using citrate as the inhibitor revealed competitive and uncompetitive inhibition patterns for G6P and F420 respectively, thus suggesting a mechanism of ordered addition of substrates in which the F420 cofactor must first bind to FGD before G6P binding. The solvent deuterium isotope effects studies yielded normal solvent kinetic isotope effects (SKIE) on kcat and kcat/Km for both G6P and F420. The proton inventory data yielded a fractionation factor of 0.37, suggesting that the single proton responsible for the observed SKIE is likely donated by Glu109 and protonates the cofactor at position N1. The steady state substrate deuterium isotope effects studies using G6P and G6P-d1 yielded KIE of 1.1 for both kcat and kcat/Km, while the pre-steady state KIE on kobs was 1.4. Because the hydride transferred to C5 of F420 was the one targeted for isotopic substitution, these KIE values provide further evidence to support our previous findings that hydride transfer is likely not rate-limiting in the FGD reaction [1].
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- 2018
5. F420-dependent glucose-6-phosphate dehydrogenase: A comprehensive review
- Author
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Alaa Aziz, Lindsay Davis, Jamariya Howard, Kayunta Johnson-Winters, Ghader Bashiri, Amina Agbonoga, Edward N. Baker, Charlene Mandimutsira, Juan Corrales, Mercy Oyugi, and Joisha Girme
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chemistry.chemical_classification ,Rhodococcus jostii ,biology ,Mutagenesis ,Dehydrogenase ,Nocardia ,biology.organism_classification ,Cofactor ,Inorganic Chemistry ,Mycobacterium tuberculosis ,chemistry.chemical_compound ,Enzyme ,chemistry ,Biochemistry ,Materials Chemistry ,biology.protein ,Glucose-6-phosphate dehydrogenase ,Physical and Theoretical Chemistry - Abstract
F420-dependent glucose-6-phosphate dehydrogenase (FGD1) catalyzes the conversion of glucose-6-phosphate (G6P) to 6-phosphogluconolactone. During the course of this reaction, the oxidized cofactor F420 is converted to its reduced form (F420H2). FGD was initially identified and studied extensively within mycobacteria prior to the more recent discovery of FGDs from Rhodococcus jostii RHA1. Another group of FGDs that utilize a variety of sugar-6-phosphates from Nocardia and Cryptosporangium arvum is also known as the FSDs. Crystal structures of FGD from the pathogens Mycobacterium tuberculosis and Rhodococcus jostii RHA1 have provided significant insight into the structural and mechanistic properties of the enzymes and have been the basis for mutagenesis, kinetic and mechanistic studies in recent years. This review discusses the role of FGD within M. tuberculosis, followed by our current understanding of the FGD catalytic mechanism. This will also be discussed with reference to the relationship between FGD and the structurally unrelated NADP+-dependent glucose-6-phosphate enzymes.
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- 2021
6. Targeting isocitrate lyase for the treatment of latent tuberculosis
- Author
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Jonathan Sperry, Ghader Bashiri, Ivanhoe K. H. Leung, Ram Prasad Bhusal, and Brooke X. C. Kwai
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0301 basic medicine ,Tuberculosis ,030106 microbiology ,Antitubercular Agents ,Glyoxylate cycle ,Disease ,Microbiology ,Mycobacterium tuberculosis ,03 medical and health sciences ,Latent Tuberculosis ,Active tb ,Drug Resistance, Bacterial ,Drug Discovery ,medicine ,Animals ,Humans ,Citrates ,Pharmacology ,biology ,Latent tuberculosis ,Glyoxylates ,Isocitrate lyase ,biology.organism_classification ,medicine.disease ,Isocitrate Lyase ,Virology ,030104 developmental biology ,Infectious disease (medical specialty) - Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that can remain dormant for many years before becoming active. One way to control and eliminate TB is the identification and treatment of latent TB, preventing infected individuals from developing active TB and thus eliminating the subsequent spread of the disease. Isocitrate lyase (ICL) is involved in the mycobacterial glyoxylate and methylisocitrate cycles. ICL is important for the growth and survival of M. tuberculosis during latent infection. ICL is not present in humans and is therefore a potential therapeutic target for the development of anti-TB agents. Here, we explore the evidence linking ICL to persistent survival of M. tuberculosis. The structure, mechanism and inhibition of the enzyme is also discussed.
- Published
- 2017
7. Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms
- Author
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Ehab N. M. Jirgis, Esther M. M. Bulloch, Jodie M. Johnston, Edward N. Baker, and Ghader Bashiri
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0301 basic medicine ,Stereochemistry ,Pyruvate Oxidase ,Reaction intermediate ,Molecular Dynamics Simulation ,Cofactor ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Biosynthesis ,Structural Biology ,Catalytic Domain ,Hydrolase ,Transferase ,Thiamine ,Molecular Biology ,chemistry.chemical_classification ,030102 biochemistry & molecular biology ,biology ,ATP synthase ,Chemistry ,Mycobacterium tuberculosis ,030104 developmental biology ,Enzyme ,Biochemistry ,Catalytic cycle ,biology.protein ,Protein Multimerization ,Protein Binding - Abstract
Menaquinone (MQ) is an essential component of the respiratory chains of many pathogenic organisms, including Mycobacterium tuberculosis (Mtb). The first committed step in MQ biosynthesis is catalyzed by 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD), a thiamin diphosphate (ThDP)-dependent enzyme. Catalysis proceeds through two covalent intermediates as the substrates 2-oxoglutarate and isochorismate are successively added to the cofactor before final cleavage of the product. We have determined a series of crystal structures of Mtb-MenD that map the binding of both substrates, visualizing each step in the MenD catalytic cycle, including both intermediates. ThDP binding induces a marked asymmetry between the coupled active sites of each dimer, and possible mechanisms of communication can be identified. The crystal structures also reveal conformational features of the two intermediates that facilitate reaction but prevent premature product release. These data fully map chemical space to inform early-stage drug discovery targeting MenD.
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- 2016
8. Regulation and Quality Control of Adiponectin Assembly by Endoplasmic Reticulum Chaperone ERp44
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Cheng Xu, Mazdak Radjainia, Yu Wang, Margaret A. Brimble, David C. Goldstone, Paul W. R. Harris, Ghader Bashiri, Lutz Hampe, and Alok K. Mitra
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Protein subunit ,Molecular Sequence Data ,Population ,Plasma protein binding ,Endoplasmic Reticulum ,Biochemistry ,Mice ,Animals ,Humans ,Amino Acid Sequence ,Protein Interaction Maps ,education ,Molecular Biology ,Peptide sequence ,education.field_of_study ,biology ,Adiponectin ,Endoplasmic reticulum ,nutritional and metabolic diseases ,Membrane Proteins ,food and beverages ,Cell Biology ,N-terminus ,HEK293 Cells ,Chaperone (protein) ,biology.protein ,Protein Multimerization ,hormones, hormone substitutes, and hormone antagonists ,Molecular Biophysics ,Molecular Chaperones ,Protein Binding - Abstract
Adiponectin, a collagenous hormone secreted abundantly from adipocytes, possesses potent antidiabetic and anti-inflammatory properties. Mediated by the conserved Cys(39) located in the variable region of the N terminus, the trimeric (low molecular weight (LMW)) adiponectin subunit assembles into different higher order complexes, e.g. hexamers (middle molecular weight (MMW)) and 12-18-mers (high molecular weight (HMW)), the latter being mostly responsible for the insulin-sensitizing activity of adiponectin. The endoplasmic reticulum (ER) chaperone ERp44 retains adiponectin in the early secretory compartment and tightly controls the oxidative state of Cys(39) and the oligomerization of adiponectin. Using cellular and in vitro assays, we show that ERp44 specifically recognizes the LMW and MMW forms but not the HMW form. Our binding assays with short peptide mimetics of adiponectin suggest that ERp44 intercepts and converts the pool of fully oxidized LMW and MMW adiponectin, but not the HMW form, into reduced trimeric precursors. These ERp44-bound precursors in the cis-Golgi may be transported back to the ER and released to enhance the population of adiponectin intermediates with appropriate oxidative state for HMW assembly, thereby underpinning the process of ERp44 quality control.
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- 2015
9. Use of a 'silver bullet' to resolve crystal lattice dislocation disorder: A cobalamin complex of Δ1-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis
- Author
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Thomas Lagautriere, Edward N. Baker, and Ghader Bashiri
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Models, Molecular ,Stereochemistry ,Dehydrogenase ,Crystal structure ,Crystallography, X-Ray ,Cobalamin ,chemistry.chemical_compound ,Bacterial Proteins ,Structural Biology ,Oxidoreductase ,Catalytic Domain ,Binding site ,Protein Structure, Quaternary ,chemistry.chemical_classification ,Hydrogen Bonding ,Mycobacterium tuberculosis ,NAD ,Small molecule ,1-Pyrroline-5-Carboxylate Dehydrogenase ,Kinetics ,Vitamin B 12 ,Crystallography ,Cross-Linking Reagents ,chemistry ,Cobalamin binding ,Crystallization ,Protein crystallization - Abstract
The use of small molecules as “silver bullets” that can bind to generate crosslinks between protein molecules has been advanced as a powerful means of enhancing success in protein crystallization (McPherson and Cudney, 2006). We have explored this approach in attempts to overcome an order–disorder phenomenon that complicated the structural analysis of the enzyme Δ1-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis (P5CDH, Mtb-PruA). Using the Silver Bullets Bio screen, we obtained new crystal packing using cobalamin as a co-crystallization agent. This crystal form did not display the order–disorder phenomenon previously encountered. Solution of the crystal structure showed that cobalamin molecules are present in the crystal contacts. Although the cobalamin binding probably does not have physiological relevance, it reflects similarities in the nucleotide-binding region of Mtb-PruA, with the nucleotide loop of cobalamin sharing the binding site for the adenine moiety of NAD+.
- Published
- 2015
10. Crystal Structures of F420-dependent Glucose-6-phosphate Dehydrogenase FGD1 Involved in the Activation of the Anti-tuberculosis Drug Candidate PA-824 Reveal the Basis of Coenzyme and Substrate Binding
- Author
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Christopher J. Squire, Edward N. Baker, Nicole J. Moreland, and Ghader Bashiri
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Protein Conformation ,Stereochemistry ,Molecular Sequence Data ,Mycobacterium smegmatis ,Antitubercular Agents ,Molecular Conformation ,Dehydrogenase ,Flavin group ,Glucosephosphate Dehydrogenase ,Crystallography, X-Ray ,Biochemistry ,Cofactor ,Substrate Specificity ,chemistry.chemical_compound ,Oxidoreductase ,Glucose-6-phosphate dehydrogenase ,Amino Acid Sequence ,Molecular Biology ,chemistry.chemical_classification ,Sequence Homology, Amino Acid ,biology ,Substrate (chemistry) ,Mycobacterium tuberculosis ,Cell Biology ,Coenzyme F420 ,Kinetics ,Enzyme ,Models, Chemical ,chemistry ,Nitroimidazoles ,biology.protein ,Protein Binding - Abstract
The modified flavin coenzyme F(420) is found in a restricted number of microorganisms. It is widely distributed in mycobacteria, however, where it is important in energy metabolism, and in Mycobacterium tuberculosis (Mtb) is implicated in redox processes related to non-replicating persistence. In Mtb, the F(420)-dependent glucose-6-phosphate dehydrogenase FGD1 provides reduced F(420) for the in vivo activation of the nitroimidazopyran prodrug PA-824, currently being developed for anti-tuberculosis therapy against both replicating and persistent bacteria. The structure of M. tuberculosis FGD1 has been determined by x-ray crystallography both in its apo state and in complex with F(420) and citrate at resolutions of 1.90 and 1.95 A(,) respectively. The structure reveals a highly specific F(420) binding mode, which is shared with several other F(420)-dependent enzymes. Citrate occupies the substrate binding pocket adjacent to F(420) and is shown to be a competitive inhibitor (IC(50) 43 microm). Modeling of the binding of the glucose 6-phosphate (G6P) substrate identifies a positively charged phosphate binding pocket and shows that G6P, like citrate, packs against the isoalloxazine moiety of F(420) and helps promote a butterfly bend conformation that facilitates F(420) reduction and catalysis.
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- 2008
11. Expression, purification and crystallization of native and selenomethionine labeled Mycobacterium tuberculosis FGD1 (Rv0407) using a Mycobacterium smegmatis expression system
- Author
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Ghader Bashiri, Nicole J. Moreland, Christopher J. Squire, and Edward N. Baker
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Mycobacterium smegmatis ,Cell Culture Techniques ,chemistry.chemical_element ,Dehydrogenase ,Glucosephosphate Dehydrogenase ,Crystallography, X-Ray ,medicine.disease_cause ,law.invention ,Mycobacterium tuberculosis ,Bacterial Proteins ,law ,FGD1 ,Escherichia coli ,medicine ,Cloning, Molecular ,Crystallization ,Selenomethionine ,biology ,biology.organism_classification ,Recombinant Proteins ,Culture Media ,chemistry ,Biochemistry ,Recombinant DNA ,Selenium ,Biotechnology - Abstract
FGD1 is an F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium tuberculosis that has been shown to be essential for activation of the anti-TB compound PA-824. Initial attempts to produce recombinant FGD1 using Escherichia coli as a host was unsuccessful, but when the alternative host Mycobacterium smegmatis was used, soluble protein yields of 7 mg/L of culture were achieved. Both native and selenomethionine-substituted FGD1 were obtained by culturing M. smegmatis in autoinduction media protocols originally developed for E. coli. Using these media afforded the advantages of decreased handling, as cultures did not require monitoring of optical density and induction, and reduced cost by removing the need for expensive ADC enrichment normally used in mycobacterial cultures. Selenomethionine was efficiently incorporated at levels required for multiwavelength anomalous diffraction experiments used in crystal structure determination. As far as we are aware this is the first protocol for preparation of selenomethionine-substituted protein in mycobacteria. Native and selenomethionine-labeled FGD1 were successfully crystallized by vapor diffusion, with the crystals diffracting to 2.1 AA resolution.
- Published
- 2007
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